Core microbiome taxa list.

Mangrove forests are fundamental coastal ecosystems for the variety of services they provide, including green-house gas regulation, coastal protection and home to a great biodiversity. Mexico is the fourth country with the largest extension of mangroves of which 60% occurs in the Yucatan Peninsula. Understanding the microbial component of mangrove forests is necessary for their critical roles in biogeochemical cycles, ecosystem health, function and restoration initiatives. Here we study the relation between the microbial community from sediments and the restoration process of mangrove forests, comparing conserved, degraded and restored mangroves along the northern coast of the Yucatan peninsula. Results showed that although each sampling site had a differentiated microbial composition, the taxa belonged predominantly to Proteobacteria (13.2–23.6%), Desulfobacterota (7.6–8.3%) and Chloroflexi (9–15.7%) phyla, and these were similar between rainy and dry seasons. Conserved mangroves showed significantly higher diversity than degraded ones, and restored mangroves recovered their microbial diversity from the degraded state (Dunn test p-value Benjamini-Hochberg adjusted = 0.0034 and 0.0071 respectively). The structure of sediment microbial β-diversity responded significantly to the mangrove conservation status and physicochemical parameters (organic carbon content, redox potential, and salinity). Taxa within Chloroflexota, Desulfobacterota and Thermoplasmatota showed significantly higher abundance in degraded mangrove samples compared to conserved ones. This study can help set a baseline that includes the microbial component in health assessment and restoration strategies of mangrove forests.